GraphXAI: Resource to support the development and evaluation of GNN explainers

GFlowNet library

Hierarchical Graph Pooling with Structure Learning

Toolkit for calling structural variants using short or long reads

Detection and genotyping of structural variants

This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.

Tools in R for the Analysis and Visualization of Intervals and Scores

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

R package for differential expression analysis in metatranscriptomics

Network Inference Toolkit

Python implementations of the Boruta all-relevant feature selection method.

Pytorch implementation of various Graph Neural Networks (GNNs) for graph classification

Data for "Understanding Isomorphism Bias in Graph Data Sets" paper.

PyTorch implementation of DGCNN

Graph convolutions in Keras with TensorFlow, PyTorch or Jax.

Machine-learning-based general bacterial promoter prediction tool.

Computes affinity between two entities based on their co-occurrence

Single sample network reconstruction in R

The reference implementation of FEATHER from the CIKM '20 paper "Characteristic Functions on Graphs: Birds of a Feather, from Statistical Descriptors to Parametric Models".

R wrapper around C++ implementation of MIDAS (Microcluster-Based Detector of Anomalies in Edge Streams)

Various scripts used at the EnvGen group, directed towards metagenomic analysis.

Dimension Reduction and Estimation Methods

MMseqs2: ultra fast and sensitive search and clustering suite

An efficient index for the colored, compacted, de Bruijn graph

Mixtures of Gaussian graphical models for model-based clustering with sparse covariance and concentration matrices

causalMGM is an R package that allow users to learn undirected and directed (causal) graphs over mixed data types (i.e., continuous and discrete variables).